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Conserved domains on  [gi|1532491334|gb|RRR73646|]
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MAG: hypothetical protein EI684_08510 [Candidatus Viridilinea halotolerans]

Protein Classification

COG3950 family protein( domain architecture ID 11467691)

COG3950 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-342 1.60e-65

Predicted ATP-binding protein involved in virulence [General function prediction only];


:

Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 211.01  E-value: 1.60e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   1 MHIQRIRISNMKSIDTLDwaIPKDQAAGWHVIIGDNGSGKSTLLRAITLALLGPVEAAGlrqdwdtwlraetksgsvrld 80
Cdd:COG3950     1 MRIKSLTIENFRGFEDLE--IDFDNPPRLTVLVGENGSGKTTLLEAIALALSGLLSRLD--------------------- 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  81 mtydpqidqftgpgrrdaemvpaavqiEYDGHKAQIKKGRETPNperhiwsgagGWFSVAYGPFRRFSGGD-APFKTQSL 159
Cdd:COG3950    58 ---------------------------DVKFRKLLIRNGEFGDS----------AKLILYYGTSRLLLDGPlKKLERLKE 100

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 160 RSLPRLAAHLSVFNEAFALSEGLRWLQELQFKRLEQLSEGmlLERLITFVNQ--KDFLPFGMRIRsIDDvGSSGIFFTDP 237
Cdd:COG3950   101 EYFSRLDGYDSLLDEDSNLREFLEWLREYLEDLENKLSDE--LDEKLEAVREalNKLLPDFKDIR-IDR-DPGRLVILDK 176

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 238 HGQRVSVENLSDGYRSILSLTFDLIRHMVNTYGpnavfdaSDPTVIHAPGVVLIDEVDAHLHPSWQKRVGFWFRQHFPHV 317
Cdd:COG3950   177 NGEELPLNQLSDGERSLLALVGDLARRLAELNP-------ALENPLEGEGIVLIDEIDLHLHPKWQRRILPDLRKIFPNI 249

                         330       340
                  ....*....|....*....|....*
gi 1532491334 318 QFIVTTHSPLVCQAATEGSIWRLPR 342
Cdd:COG3950   250 QFIVTTHSPLILSSLEDEEVIVLER 274
DppF super family cl34123
ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid ...
 32-101 6.13e-05

ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism, Inorganic ion transport and metabolism];


The actual alignment was detected with superfamily member COG1124:

Pssm-ID: 440741 [Multi-domain]  Cd Length: 248  Bit Score: 44.41  E-value: 6.13e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  32 IIGDNGSGKSTLLRAItlallgpveaAGLRQDWdtwlraetkSGSVRLDMTydPQIDQFTGPGRRDAEMV 101
Cdd:COG1124    36 LVGESGSGKSTLLRAL----------AGLERPW---------SGEVTFDGR--PVTRRRRKAFRRRVQMV 84
 
Name Accession Description Interval E-value
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-342 1.60e-65

Predicted ATP-binding protein involved in virulence [General function prediction only];


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 211.01  E-value: 1.60e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   1 MHIQRIRISNMKSIDTLDwaIPKDQAAGWHVIIGDNGSGKSTLLRAITLALLGPVEAAGlrqdwdtwlraetksgsvrld 80
Cdd:COG3950     1 MRIKSLTIENFRGFEDLE--IDFDNPPRLTVLVGENGSGKTTLLEAIALALSGLLSRLD--------------------- 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  81 mtydpqidqftgpgrrdaemvpaavqiEYDGHKAQIKKGRETPNperhiwsgagGWFSVAYGPFRRFSGGD-APFKTQSL 159
Cdd:COG3950    58 ---------------------------DVKFRKLLIRNGEFGDS----------AKLILYYGTSRLLLDGPlKKLERLKE 100

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 160 RSLPRLAAHLSVFNEAFALSEGLRWLQELQFKRLEQLSEGmlLERLITFVNQ--KDFLPFGMRIRsIDDvGSSGIFFTDP 237
Cdd:COG3950   101 EYFSRLDGYDSLLDEDSNLREFLEWLREYLEDLENKLSDE--LDEKLEAVREalNKLLPDFKDIR-IDR-DPGRLVILDK 176

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 238 HGQRVSVENLSDGYRSILSLTFDLIRHMVNTYGpnavfdaSDPTVIHAPGVVLIDEVDAHLHPSWQKRVGFWFRQHFPHV 317
Cdd:COG3950   177 NGEELPLNQLSDGERSLLALVGDLARRLAELNP-------ALENPLEGEGIVLIDEIDLHLHPKWQRRILPDLRKIFPNI 249

                         330       340
                  ....*....|....*....|....*
gi 1532491334 318 QFIVTTHSPLVCQAATEGSIWRLPR 342
Cdd:COG3950   250 QFIVTTHSPLILSSLEDEEVIVLER 274
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 30-328 1.19e-20

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.


Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 91.68  E-value: 1.19e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  30 HVIIGDNGSGKSTLLRAitLALLGPVEAAGLRQDWDTWLRAETKSGSVRLDMTYDPQIDQFTGPGRRDAEMVpaaVQIEY 109
Cdd:pfam13304   2 NVLIGPNGSGKSNLLEA--LRFLADFDALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVR---YRYGL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 110 DGHKAQIK-KGRETPNPERHIWS-------GAGGWFSVAYGPFRRFSGGDAPFKT-------QSLRSLPRLAAHLSVFNE 174
Cdd:pfam13304  77 DLEREDVEeKLSSKPTLLEKRLLlredseeREPKFPPEAEELRLGLDVEERIELSlselsdlISGLLLLSIISPLSFLLL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 175 AFALSEGLRWLQELQFKRLE-QLSEGMLLERLITFVNQKDFLPFGMRIRSID-------DVGSSGIFFTDPHGQRVSVEN 246
Cdd:pfam13304 157 LDEGLLLEDWAVLDLAADLAlFPDLKELLQRLVRGLKLADLNLSDLGEGIEKsllvddrLRERGLILLENGGGGELPAFE 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 247 LSDGYRSILSLTFDLIRhmvntygpnavfdasdptVIHAPGVVLIDEVDAHLHPSWQKRVGFWFRQ-HFPHVQFIVTTHS 325
Cdd:pfam13304 237 LSDGTKRLLALLAALLS------------------ALPKGGLLLIDEPESGLHPKLLRRLLELLKElSRNGAQLILTTHS 298


                  ...
gi 1532491334 326 PLV 328
Cdd:pfam13304 299 PLL 301
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-53 2.28e-05

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 46.96  E-value: 2.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1532491334   1 MHIQRIRISNMKSIDTLDWAIPKdqaaGWHVIIGDNGSGKSTLLRAITLALLG 53
Cdd:PRK02224    1 MRFDRVRLENFKCYADADLRLED----GVTVIHGVNGSGKSSLLEACFFALYG 49
ABC_SMC2_euk cd03273
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ...
 243-321 5.58e-05

ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213240 [Multi-domain]  Cd Length: 251  Bit Score: 44.60  E-value: 5.58e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1532491334 243 SVENLSDGYRSILSLTfdLIRHMVnTYGPnavfdasdptvihAPgVVLIDEVDAHLHPSWQKRVGFWFRQHFPHVQFIV 321
Cdd:cd03273   163 SLTELSGGQRSLVALS--LILALL-LFKP-------------AP-MYILDEVDAALDLSHTQNIGRMIKTHFKGSQFIV 224
DppF COG1124
ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid ...
 32-101 6.13e-05

ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism, Inorganic ion transport and metabolism];


Pssm-ID: 440741 [Multi-domain]  Cd Length: 248  Bit Score: 44.41  E-value: 6.13e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  32 IIGDNGSGKSTLLRAItlallgpveaAGLRQDWdtwlraetkSGSVRLDMTydPQIDQFTGPGRRDAEMV 101
Cdd:COG1124    36 LVGESGSGKSTLLRAL----------AGLERPW---------SGEVTFDGR--PVTRRRRKAFRRRVQMV 84
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 1-59 5.82e-04

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 42.26  E-value: 5.82e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1532491334    1 MHIQRIRISNMKSIDTlDWAIPKDQAAGWHVIIGDNGSGKSTLLRAITLALLGPVEAAG 59
Cdd:TIGR00618    1 MKPLRLTLKNFGSYKG-THTIDFTALGPIFLICGKTGAGKTTLLDAITYALYGKLPRRS 58
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 31-90 1.28e-03

ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213244 [Multi-domain]  Cd Length: 213  Bit Score: 39.89  E-value: 1.28e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1532491334  31 VIIGDNGSGKSTLLRAITLALLGPVEAAGLRQDWDTWLRAETKSGSVRLDMTYDP---QID---QF 90
Cdd:cd03277    27 MIIGPNGSGKSSIVCAICLGLGGKPKLLGRAKKVGEFVKRGCDEGTIEIELYGNPgniQVDnlcQF 92
 
Name Accession Description Interval E-value
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-342 1.60e-65

Predicted ATP-binding protein involved in virulence [General function prediction only];


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 211.01  E-value: 1.60e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   1 MHIQRIRISNMKSIDTLDwaIPKDQAAGWHVIIGDNGSGKSTLLRAITLALLGPVEAAGlrqdwdtwlraetksgsvrld 80
Cdd:COG3950     1 MRIKSLTIENFRGFEDLE--IDFDNPPRLTVLVGENGSGKTTLLEAIALALSGLLSRLD--------------------- 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  81 mtydpqidqftgpgrrdaemvpaavqiEYDGHKAQIKKGRETPNperhiwsgagGWFSVAYGPFRRFSGGD-APFKTQSL 159
Cdd:COG3950    58 ---------------------------DVKFRKLLIRNGEFGDS----------AKLILYYGTSRLLLDGPlKKLERLKE 100

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 160 RSLPRLAAHLSVFNEAFALSEGLRWLQELQFKRLEQLSEGmlLERLITFVNQ--KDFLPFGMRIRsIDDvGSSGIFFTDP 237
Cdd:COG3950   101 EYFSRLDGYDSLLDEDSNLREFLEWLREYLEDLENKLSDE--LDEKLEAVREalNKLLPDFKDIR-IDR-DPGRLVILDK 176

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 238 HGQRVSVENLSDGYRSILSLTFDLIRHMVNTYGpnavfdaSDPTVIHAPGVVLIDEVDAHLHPSWQKRVGFWFRQHFPHV 317
Cdd:COG3950   177 NGEELPLNQLSDGERSLLALVGDLARRLAELNP-------ALENPLEGEGIVLIDEIDLHLHPKWQRRILPDLRKIFPNI 249

                         330       340
                  ....*....|....*....|....*
gi 1532491334 318 QFIVTTHSPLVCQAATEGSIWRLPR 342
Cdd:COG3950   250 QFIVTTHSPLILSSLEDEEVIVLER 274
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-328 1.67e-21

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 95.07  E-value: 1.67e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   1 MHIQRIRISNMKSIDTLDWAIPKDQAagwhVIIGDNGSGKSTLLRAITLaLLGPVEAAGLRQDwDTWLRAETKSGSVRLD 80
Cdd:COG3593     1 MKLEKIKIKNFRSIKDLSIELSDDLT----VLVGENNSGKSSILEALRL-LLGPSSSRKFDEE-DFYLGDDPDLPEIEIE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  81 MTYDPQIDQFTGpgrrdaemvpaavQIEYDGHKAQIKKGRETPNPErhiwsgaggwfsvaygpfrrfsggdapfktqslr 160
Cdd:COG3593    75 LTFGSLLSRLLR-------------LLLKEEDKEELEEALEELNEE---------------------------------- 107

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 161 slprlaahlsvFNEAF-ALSEGLRwlqelqfKRLEQLSEGMLLERLITFVNQKDFLpfgmriRSIDdvgssgIFFTDphG 239
Cdd:COG3593   108 -----------LKEALkALNELLS-------EYLKELLDGLDLELELSLDELEDLL------KSLS------LRIED--G 155

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 240 QRVSVENLSDGYRSILSLTFDLIRHMVNTYGPNAVFdasdptvihapgvvLIDEVDAHLHPSWQKRvgfwFRQHF----- 314
Cdd:COG3593   156 KELPLDRLGSGFQRLILLALLSALAELKRAPANPIL--------------LIEEPEAHLHPQAQRR----LLKLLkelse 217

                         330
                  ....*....|....
gi 1532491334 315 PHVQFIVTTHSPLV 328
Cdd:COG3593   218 KPNQVIITTHSPHL 231
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 30-328 1.19e-20

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.


Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 91.68  E-value: 1.19e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  30 HVIIGDNGSGKSTLLRAitLALLGPVEAAGLRQDWDTWLRAETKSGSVRLDMTYDPQIDQFTGPGRRDAEMVpaaVQIEY 109
Cdd:pfam13304   2 NVLIGPNGSGKSNLLEA--LRFLADFDALVIGLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVR---YRYGL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 110 DGHKAQIK-KGRETPNPERHIWS-------GAGGWFSVAYGPFRRFSGGDAPFKT-------QSLRSLPRLAAHLSVFNE 174
Cdd:pfam13304  77 DLEREDVEeKLSSKPTLLEKRLLlredseeREPKFPPEAEELRLGLDVEERIELSlselsdlISGLLLLSIISPLSFLLL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 175 AFALSEGLRWLQELQFKRLE-QLSEGMLLERLITFVNQKDFLPFGMRIRSID-------DVGSSGIFFTDPHGQRVSVEN 246
Cdd:pfam13304 157 LDEGLLLEDWAVLDLAADLAlFPDLKELLQRLVRGLKLADLNLSDLGEGIEKsllvddrLRERGLILLENGGGGELPAFE 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 247 LSDGYRSILSLTFDLIRhmvntygpnavfdasdptVIHAPGVVLIDEVDAHLHPSWQKRVGFWFRQ-HFPHVQFIVTTHS 325
Cdd:pfam13304 237 LSDGTKRLLALLAALLS------------------ALPKGGLLLIDEPESGLHPKLLRRLLELLKElSRNGAQLILTTHS 298


                  ...
gi 1532491334 326 PLV 328
Cdd:pfam13304 299 PLL 301
COG4637 COG4637
Predicted ATPase [General function prediction only];
3-340 4.73e-17

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 82.29  E-value: 4.73e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   3 IQRIRISNMKSIDTLDWAIPkdqaaGWHVIIGDNGSGKSTLLRAITL---ALLGPVEAAGLRQ---DWDTWLRAETKSGS 76
Cdd:COG4637     2 ITRIRIKNFKSLRDLELPLG-----PLTVLIGANGSGKSNLLDALRFlsdAARGGLQDALARRgglEELLWRGPRTITEP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  77 VRLDMTYDPqidqftgpgrRDAEMVPAAVQIEYDGHKAQIKKGRETpnperhIWSGAGGWfsvaYGPF--RRFSGGDAPF 154
Cdd:COG4637    77 IRLELEFAE----------EDERDLRYELELGLPEPGGRPEVKEER------LWLKRGSG----GRPFldFRPKGRAVGG 136

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 155 KTQSLRSLPRLAAHL---SVFNEAFALSEGLR---------------------------------WLQELQFKRLEQLSE 198
Cdd:COG4637   137 EPERLDSPESLLSQLgdpERFPELRALREALRswrfydfhpaplrqpqpagrtpvlapdgsnlaaVLATLRETHPERFER 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 199 gmLLERLitfvnqKDFLPFgmrIRSIDDVGSSG----IFFTDPHGQR-VSVENLSDGYRSILSLTfdlirhmvntygpNA 273
Cdd:COG4637   217 --ILEAL------RDAFPG---FEDIEVEPDEDgrvlLEFREKGLDRpFPARELSDGTLRFLALL-------------AA 272

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1532491334 274 VFDAsdptviHAPGVVLIDEVDAHLHPSWQKRVGFWFRQHFPHVQFIVTTHSPLVCQAATEGSIWRL 340
Cdd:COG4637   273 LLSP------RPPPLLCIEEPENGLHPDLLPALAELLREASERTQVIVTTHSPALLDALEPEEVLVL 333
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
2-340 7.89e-13

ATPase/GTPase, AAA15 family [General function prediction only];


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 68.92  E-value: 7.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   2 HIQRIRISNMKSID---TLDWAIPKDQAAGWHVIIGDNGSGKSTLLRAITLaLLGPVEaaglrqdwdtwlraetkSGSVR 78
Cdd:COG1106     1 MLISFSIENFRSFKdelTLSMVASGLRLLRVNLIYGANASGKSNLLEALYF-LRNLVL-----------------NSSQP 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  79 LDMTYDPQIDqftgpgRRDAEMVPAAVQIEY--DGHKAQIkkgretpnperhiwsgaggwfsvaygpfrRFSGGDAPFKT 156
Cdd:COG1106    63 GDKLVEPFLL------DSESKNEPSEFEILFllDGVRYEY-----------------------------GFELDKERIIS 107

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 157 QSLRSLPRLAAH-LSVFNEAF-ALSEGLRWLQELQFKRLEQLSEGMLLERLITFVNQKDFLPFGMRIR--SIDDVGSSGI 232
Cdd:COG1106   108 EWLYFLSTAAQLnVPLLSPLYdWFDNNISLDTSSDGLTLLLKEDESLKEELLELLKIADPGIEDIEVEeeEIEDLVERKL 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 233 FFTD-PHGQRVSVENLSDGYRSIlsltFDLIRHMVNtygpnavfdasdptVIHAPGVVLIDEVDAHLHPSWQKRVGFWFR 311
Cdd:COG1106   188 IFKHkGGNVPLPLSEESDGTKRL----LALAGALLD--------------ALAKGGVLLIDEIEASLHPSLLRKLLKLFL 249

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 1532491334 312 QHFP--HVQFIVTTHSPL----VCQAATEGSIWRL 340
Cdd:COG1106   250 DLANknNAQLIFTTHSTElldaFLELLRRDQIWFV 284
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-100 4.23e-10

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 59.25  E-value: 4.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   2 HIQRIRISNMKSI---DTLDWAipkdqaAGWHVIIGDNGSGKSTLLRAITLALLGPVEAAGlrQDWDTWLRAETKSGSVR 78
Cdd:COG0419     1 KLLRLRLENFRSYrdtETIDFD------DGLNLIVGPNGAGKSTILEAIRYALYGKARSRS--KLRSDLINVGSEEASVE 72

                          90       100
                  ....*....|....*....|..
gi 1532491334  79 LDMTYDPQIDQFTgpgRRDAEM 100
Cdd:COG0419    73 LEFEHGGKRYRIE---RRQGEF 91
COG4938 COG4938
Predicted ATPase [General function prediction only];
158-326 4.23e-09

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 57.29  E-value: 4.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 158 SLRSLPRL--AAHLSVFNEAFALSEGLR-WLQELQFKRLEQLSEGMLLERLITFVNqkDFLPFGMRIRSIDDVGSSgIFF 234
Cdd:COG4938    53 AERSGPARlyPSLVRELSDLGSRGEYTAdFLAELENLEILDDKSKELLEQVEEWLE--KIFPGKVEVDASSDLVRL-VFR 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 235 TDPHGQRVSVENLSDGYRSILSLTFdlirhmvntygpnAVFDASDPTVIhapgvVLIDEVDAHLHPSWQKRVGfwfrQHF 314
Cdd:COG4938   130 PSGNGKRIPLSNVGSGVSELLPILL-------------ALLSAAKPGSL-----LIIEEPEAHLHPKAQSALA----ELL 187

                         170
                  ....*....|....*..
gi 1532491334 315 P-----HVQFIVTTHSP 326
Cdd:COG4938   188 AelansGVQVIIETHSD 204
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 185-324 5.96e-08

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 54.98  E-value: 5.96e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  185 LQELQFKRLEQLSEGMLLERLIT----FVNQKDFLP--FGMRIRSIDDVGSSGI-FFTDPHGQRV-SVENLSDGYRSILS 256
Cdd:pfam02463 1008 IRAIIEETCQRLKEFLELFVSINkgwnKVFFYLELGgsAELRLEDPDDPFSGGIeISARPPGKGVkNLDLLSGGEKTLVA 1087

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1532491334  257 LTFDLIRHMvntYGPnavfdasdptvihAPGVVLiDEVDAHLHPSWQKRVGFWFRQHFPHVQFIVTTH 324
Cdd:pfam02463 1088 LALIFAIQK---YKP-------------APFYLL-DEIDAALDDQNVSRVANLLKELSKNAQFIVISL 1138
AAA_23 pfam13476
AAA domain;
31-83 3.18e-06

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 47.49  E-value: 3.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1532491334  31 VIIGDNGSGKSTLLRAITLALLGPVEAAGlRQDWDTWLRAETKSGSVRLDMTY 83
Cdd:pfam13476  22 LITGPNGSGKTTILDAIKLALYGKTSRLK-RKSGGGFVKGDIRIGLEGKGKAY 73
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 177-326 4.11e-06

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433011 [Multi-domain]  Cd Length: 392  Bit Score: 48.75  E-value: 4.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 177 ALSEGLRWLQELQFKRLEQLSEgmLLERLITFVNQKDFLPFGMRIRSIDDVGSSGIFFTDPHGQRVSVENLSD------- 249
Cdd:pfam13175 240 LLGALKQRIFEEALQEELELTE--KLKETQNKLKEIDKTLAEELKNILFKKIDKLKDFGYPPFLNPEIEIKKDdedlpln 317

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334 250 ----GYRSILSLTFDLIRhmvntygpNAVFDASDPTVIHapgVVLIDEVDAHLHPSWQKRvgfwFRQHF------PHVQF 319
Cdd:pfam13175 318 kngsGVQRLILLIFFIAE--------AERKEDEIEEKNV---ILAIEEPEAHLHPQAQRV----LIKLLkelandNKTQV 382


                  ....*..
gi 1532491334 320 IVTTHSP 326
Cdd:pfam13175 383 IITTHSP 389
AAA_29 pfam13555
P-loop containing region of AAA domain;
4-54 1.15e-05

P-loop containing region of AAA domain;


Pssm-ID: 433304 [Multi-domain]  Cd Length: 61  Bit Score: 42.59  E-value: 1.15e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1532491334   4 QRIRISNMKSIDTLDWAIPKdqaAGWHVIIGDNGSGKSTLLRAITLALLGP 54
Cdd:pfam13555   2 TRLQLINWGTFDGHTIPIDP---RGNTLLTGPSGSGKSTLLDAIQTLLVPA 49
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-53 2.28e-05

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 46.96  E-value: 2.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1532491334   1 MHIQRIRISNMKSIDTLDWAIPKdqaaGWHVIIGDNGSGKSTLLRAITLALLG 53
Cdd:PRK02224    1 MRFDRVRLENFKCYADADLRLED----GVTVIHGVNGSGKSSLLEACFFALYG 49
ABC_SMC2_euk cd03273
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ...
 243-321 5.58e-05

ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213240 [Multi-domain]  Cd Length: 251  Bit Score: 44.60  E-value: 5.58e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1532491334 243 SVENLSDGYRSILSLTfdLIRHMVnTYGPnavfdasdptvihAPgVVLIDEVDAHLHPSWQKRVGFWFRQHFPHVQFIV 321
Cdd:cd03273   163 SLTELSGGQRSLVALS--LILALL-LFKP-------------AP-MYILDEVDAALDLSHTQNIGRMIKTHFKGSQFIV 224
DppF COG1124
ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid ...
 32-101 6.13e-05

ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism, Inorganic ion transport and metabolism];


Pssm-ID: 440741 [Multi-domain]  Cd Length: 248  Bit Score: 44.41  E-value: 6.13e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334  32 IIGDNGSGKSTLLRAItlallgpveaAGLRQDWdtwlraetkSGSVRLDMTydPQIDQFTGPGRRDAEMV 101
Cdd:COG1124    36 LVGESGSGKSTLLRAL----------AGLERPW---------SGEVTFDGR--PVTRRRRKAFRRRVQMV 84
FepC COG1120
ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component [Inorganic ion ...
 17-80 8.50e-05

ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component [Inorganic ion transport and metabolism, Coenzyme transport and metabolism];


Pssm-ID: 440737 [Multi-domain]  Cd Length: 254  Bit Score: 43.88  E-value: 8.50e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1532491334  17 LDWAIPKDQaagWHVIIGDNGSGKSTLLRAItlallgpveaAGLrqdwdtwLRAetKSGSVRLD 80
Cdd:COG1120    20 VSLSLPPGE---VTALLGPNGSGKSTLLRAL----------AGL-------LKP--SSGEVLLD 61
ABC_sbcCD cd03279
ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are ...
 31-80 1.25e-04

ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.


Pssm-ID: 213246 [Multi-domain]  Cd Length: 213  Bit Score: 43.03  E-value: 1.25e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1532491334  31 VIIGDNGSGKSTLLRAITLALLGPVEAAGLRQDWDTWLRAETKSGSVRLD 80
Cdd:cd03279    32 LICGPTGAGKSTILDAITYALYGKTPRYGRQENLRSVFAPGEDTAEVSFT 81
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-53 1.30e-04

Recombinational DNA repair ATPase RecF [Replication, recombination and repair];


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 43.99  E-value: 1.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1532491334   2 HIQRIRISNMKSIDTLDWAIPkdqaAGWHVIIGDNGSGKSTLLRAITLALLG 53
Cdd:COG1195     1 RLKRLSLTNFRNYESLELEFS----PGINVLVGPNGQGKTNLLEAIYLLATG 48
ABC_tran pfam00005
ABC transporter; ABC transporters for a large family of proteins responsible for translocation ...
 14-48 1.86e-04

ABC transporter; ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong in different polypeptide chains.


Pssm-ID: 394964 [Multi-domain]  Cd Length: 150  Bit Score: 41.48  E-value: 1.86e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1532491334  14 IDTLDWAIPKDQaagWHVIIGDNGSGKSTLLRAIT 48
Cdd:pfam00005   1 LKNVSLTLNPGE---ILALVGPNGAGKSTLLKLIA 32
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 5-51 1.95e-04

ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 41.46  E-value: 1.95e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1532491334   5 RIRISNMKSIDTLDWAIPKDQaagWHVIIGDNGSGKSTLLRAITLAL 51
Cdd:cd00267     6 SFRYGGRTALDNVSLTLKAGE---IVALVGPNGSGKSTLLRAIAGLL 49
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 31-53 3.54e-04

ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 40.81  E-value: 3.54e-04
                          10        20
                  ....*....|....*....|...
gi 1532491334  31 VIIGDNGSGKSTLLRAITLALLG 53
Cdd:cd03227    25 IITGPNGSGKSTILDAIGLALGG 47
TagH COG1134
ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate ...
 32-48 4.21e-04

ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism];


Pssm-ID: 440749 [Multi-domain]  Cd Length: 245  Bit Score: 41.61  E-value: 4.21e-04
                          10
                  ....*....|....*..
gi 1532491334  32 IIGDNGSGKSTLLRAIT 48
Cdd:COG1134    57 IIGRNGAGKSTLLKLIA 73
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 2-63 4.49e-04

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 42.65  E-value: 4.49e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1532491334    2 HIQRIRISNMKSI-DTLDWAIPKdqaaGWHVIIGDNGSGKSTLLRAItLALLGPVEAAGLRQD 63
Cdd:pfam02463    1 YLKRIEIEGFKSYaKTVILPFSP----GFTAIVGPNGSGKSNILDAI-LFVLGERSAKSLRSE 58
ModF COG1119
ABC-type molybdenum transport system, ATPase component ModF/photorepair protein PhrA ...
 14-48 5.71e-04

ABC-type molybdenum transport system, ATPase component ModF/photorepair protein PhrA [Inorganic ion transport and metabolism];


Pssm-ID: 440736 [Multi-domain]  Cd Length: 250  Bit Score: 41.22  E-value: 5.71e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1532491334  14 IDTLDWAIPKDQaagwH-VIIGDNGSGKSTLLRAIT 48
Cdd:COG1119    19 LDDISWTVKPGE----HwAILGPNGAGKSTLLSLIT 50
recF PRK00064
recombination protein F; Reviewed
 1-61 5.76e-04

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 41.68  E-value: 5.76e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1532491334   1 MHIQRIRISNMKSIDTLDWAIpkdqAAGWHVIIGDNGSGKSTLLRAI-TLALLGpveaaGLR 61
Cdd:PRK00064    1 MYLTRLSLTDFRNYEELDLEL----SPGVNVLVGENGQGKTNLLEAIyLLAPGR-----SHR 53
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 1-59 5.82e-04

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 42.26  E-value: 5.82e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1532491334    1 MHIQRIRISNMKSIDTlDWAIPKDQAAGWHVIIGDNGSGKSTLLRAITLALLGPVEAAG 59
Cdd:TIGR00618    1 MKPLRLTLKNFGSYKG-THTIDFTALGPIFLICGKTGAGKTTLLDAITYALYGKLPRRS 58
COG3910 COG3910
Predicted ATPase [General function prediction only];
31-51 6.09e-04

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 41.29  E-value: 6.09e-04
                          10        20
                  ....*....|....*....|.
gi 1532491334  31 VIIGDNGSGKSTLLRAITLAL 51
Cdd:COG3910    41 FFVGENGSGKSTLLEAIAVAA 61
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-80 7.46e-04

ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.


Pssm-ID: 213207 [Multi-domain]  Cd Length: 204  Bit Score: 40.67  E-value: 7.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   3 IQRIRISNMKSIDtldwaipKDQA----AGWHVIIGDNGSGKSTLLRAITLALLG--PVEAAGLRQDwDTWLRAETKSGS 76
Cdd:cd03240     1 IDKLSIRNIRSFH-------ERSEieffSPLTLIVGQNGAGKTTIIEALKYALTGelPPNSKGGAHD-PKLIREGEVRAQ 72


                  ....
gi 1532491334  77 VRLD 80
Cdd:cd03240    73 VKLA 76
ABC_cobalt_CbiO_domain1 cd03225
First domain of the ATP-binding cassette component of cobalt transport system; Domain I of the ...
 31-54 7.95e-04

First domain of the ATP-binding cassette component of cobalt transport system; Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.


Pssm-ID: 213192 [Multi-domain]  Cd Length: 211  Bit Score: 40.53  E-value: 7.95e-04
                          10        20
                  ....*....|....*....|....
gi 1532491334  31 VIIGDNGSGKSTLLRAITlALLGP 54
Cdd:cd03225    31 LIVGPNGSGKSTLLRLLN-GLLGP 53
ABCF_EF-3 cd03221
ATP-binding cassette domain of elongation factor 3, subfamily F; Elongation factor 3 (EF-3) is ...
 28-48 8.29e-04

ATP-binding cassette domain of elongation factor 3, subfamily F; Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.


Pssm-ID: 213188 [Multi-domain]  Cd Length: 144  Bit Score: 39.35  E-value: 8.29e-04
                          10        20
                  ....*....|....*....|..
gi 1532491334  28 GWHV-IIGDNGSGKSTLLRAIT 48
Cdd:cd03221    26 GDRIgLVGRNGAGKSTLLKLIA 47
ABC_Iron-Siderophores_B12_Hemin cd03214
ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related ...
 32-80 8.73e-04

ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.


Pssm-ID: 213181 [Multi-domain]  Cd Length: 180  Bit Score: 40.11  E-value: 8.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1532491334  32 IIGDNGSGKSTLLRAItlallgpveaAGLRqdwdtwlraETKSGSVRLD 80
Cdd:cd03214    30 ILGPNGAGKSTLLKTL----------AGLL---------KPSSGEILLD 59
ABCD_peroxisomal_ALDP cd03223
ATP-binding cassette domain of peroxisomal transporter, subfamily D; Peroxisomal ATP-binding ...
 14-47 1.06e-03

ATP-binding cassette domain of peroxisomal transporter, subfamily D; Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).


Pssm-ID: 213190 [Multi-domain]  Cd Length: 166  Bit Score: 39.44  E-value: 1.06e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1532491334  14 IDTLDWAIPkdqAAGWHVIIGDNGSGKSTLLRAI 47
Cdd:cd03223    17 LKDLSFEIK---PGDRLLITGPSGTGKSSLFRAL 47
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 31-90 1.28e-03

ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213244 [Multi-domain]  Cd Length: 213  Bit Score: 39.89  E-value: 1.28e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1532491334  31 VIIGDNGSGKSTLLRAITLALLGPVEAAGLRQDWDTWLRAETKSGSVRLDMTYDP---QID---QF 90
Cdd:cd03277    27 MIIGPNGSGKSSIVCAICLGLGGKPKLLGRAKKVGEFVKRGCDEGTIEIELYGNPgniQVDnlcQF 92
CcmA COG4133
ABC-type transport system involved in cytochrome c biogenesis, ATPase component ...
 26-80 1.35e-03

ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443308 [Multi-domain]  Cd Length: 206  Bit Score: 39.77  E-value: 1.35e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1532491334  26 AAG-WHVIIGDNGSGKSTLLRAItlallgpveaAGLrqdwdtwLRAEtkSGSVRLD 80
Cdd:COG4133    26 AAGeALALTGPNGSGKTTLLRIL----------AGL-------LPPS--AGEVLWN 62
ZnuC COG1121
ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]; ...
 32-56 1.45e-03

ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism];


Pssm-ID: 440738 [Multi-domain]  Cd Length: 245  Bit Score: 40.07  E-value: 1.45e-03
                          10        20
                  ....*....|....*....|....*
gi 1532491334  32 IIGDNGSGKSTLLRAItLALLGPVE 56
Cdd:COG1121    37 IVGPNGAGKSTLLKAI-LGLLPPTS 60
EcfA2 COG1122
Energy-coupling factor transporter ATP-binding protein EcfA2 [Inorganic ion transport and ...
 29-56 1.45e-03

Energy-coupling factor transporter ATP-binding protein EcfA2 [Inorganic ion transport and metabolism, General function prediction only];


Pssm-ID: 440739 [Multi-domain]  Cd Length: 230  Bit Score: 40.01  E-value: 1.45e-03
                          10        20
                  ....*....|....*....|....*...
gi 1532491334  29 WHVIIGDNGSGKSTLLRAITlALLGPVE 56
Cdd:COG1122    29 FVAIIGPNGSGKSTLLRLLN-GLLKPTS 55
Uup COG0488
ATPase components of ABC transporters with duplicated ATPase domains [General function ...
 14-48 1.62e-03

ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only];


Pssm-ID: 440254 [Multi-domain]  Cd Length: 520  Bit Score: 40.82  E-value: 1.62e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1532491334  14 IDTLDWAIPKDQAAGwhvIIGDNGSGKSTLLRAIT 48
Cdd:COG0488   331 LDDLSLRIDRGDRIG---LIGPNGAGKSTLLKLLA 362
46 PHA02562
endonuclease subunit; Provisional
 32-53 1.75e-03

endonuclease subunit; Provisional


Pssm-ID: 222878 [Multi-domain]  Cd Length: 562  Bit Score: 40.77  E-value: 1.75e-03
                          10        20
                  ....*....|....*....|..
gi 1532491334  32 IIGDNGSGKSTLLRAITLALLG 53
Cdd:PHA02562   32 ITGKNGAGKSTMLEALTFALFG 53
ABC_Metallic_Cations cd03235
ATP-binding cassette domain of the metal-type transporters; This family includes transporters ...
 32-54 1.96e-03

ATP-binding cassette domain of the metal-type transporters; This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.


Pssm-ID: 213202 [Multi-domain]  Cd Length: 213  Bit Score: 39.44  E-value: 1.96e-03
                          10        20
                  ....*....|....*....|...
gi 1532491334  32 IIGDNGSGKSTLLRAItLALLGP 54
Cdd:cd03235    30 IVGPNGAGKSTLLKAI-LGLLKP 51
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
32-54 2.66e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 40.28  E-value: 2.66e-03
                           10        20
                   ....*....|....*....|...
gi 1532491334   32 IIGDNGSGKSTLLRAITLALLGP 54
Cdd:COG4913     29 LTGDNGSGKSTLLDAIQTLLVPA 51
ABC_FeS_Assembly cd03217
ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Biosynthesis of ...
 30-47 2.70e-03

ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Biosynthesis of iron-sulfur clusters (Fe-S) depends on multi-protein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.


Pssm-ID: 213184 [Multi-domain]  Cd Length: 200  Bit Score: 38.66  E-value: 2.70e-03
                          10
                  ....*....|....*...
gi 1532491334  30 HVIIGDNGSGKSTLLRAI 47
Cdd:cd03217    29 HALMGPNGSGKSTLAKTI 46
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-63 2.75e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.05  E-value: 2.75e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   1 MHIQRIRISNMKS-----IDTLDwaipkdqaaGWHVIIGDNGSGKSTLLRAITLALLG--PVEAAGLRQD 63
Cdd:PRK03918    1 MKIEELKIKNFRShkssvVEFDD---------GINLIIGQNGSGKSSILEAILVGLYWghGSKPKGLKKD 61
MK0520 COG2401
ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction ...
 31-67 2.77e-03

ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only];


Pssm-ID: 441957 [Multi-domain]  Cd Length: 222  Bit Score: 39.17  E-value: 2.77e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1532491334  31 VIIGDNGSGKSTLLRAITLALLGPVEAAGLRQDWDTW 67
Cdd:COG2401    60 LIVGASGSGKSTLLRLLAGALKGTPVAGCVDVPDNQF 96
recF PRK14079
recombination protein F; Provisional
 1-75 2.84e-03

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 39.77  E-value: 2.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1532491334   1 MHIQRIRISNMKSIDTLDWAIPkdqaAGWHVIIGDNGSGKSTLLRAITLALLGPVEAAGLRQ-----DWDTWLRAETKSG 75
Cdd:PRK14079    1 MRLLSLRQLNYRNLAPPTLAFP----PGVTAVVGENAAGKTNLLEAIYLALTGELPNGRLADlvrfgEGEAWVHAEVETG 76
hmuV PRK13548
hemin importer ATP-binding subunit; Provisional
 31-48 4.82e-03

hemin importer ATP-binding subunit; Provisional


Pssm-ID: 237422 [Multi-domain]  Cd Length: 258  Bit Score: 38.60  E-value: 4.82e-03
                          10
                  ....*....|....*...
gi 1532491334  31 VIIGDNGSGKSTLLRAIT 48
Cdd:PRK13548   32 AILGPNGAGKSTLLRALS 49
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 32-51 5.79e-03

ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213243 [Multi-domain]  Cd Length: 198  Bit Score: 37.96  E-value: 5.79e-03
                          10        20
                  ....*....|....*....|
gi 1532491334  32 IIGDNGSGKSTLLRAITLAL 51
Cdd:cd03276    26 IVGNNGSGKSAILTALTIGL 45
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 290-334 6.64e-03

The SMC head domain belongs to the ATP-binding cassette superfamily; The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.


Pssm-ID: 213206 [Multi-domain]  Cd Length: 178  Bit Score: 37.29  E-value: 6.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1532491334 290 LIDEVDAHLHPSWQKRVGFWFRQHFPHV-QFIVTTHSPLVCQAATE 334
Cdd:cd03239   121 VLDEIDAALDPTNRRRVSDMIKEMAKHTsQFIVITLKKEMFENADK 166
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-53 6.71e-03

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 38.73  E-value: 6.71e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1532491334   1 MHIQRIRISNMKSIDtlDWAIPKDqaAGWHVIIGDNGSGKSTLLRAITLALLG 53
Cdd:PRK01156    1 MIIKRIRLKNFLSHD--DSEIEFD--TGINIITGKNGAGKSSIVDAIRFALFT 49
PRK13539 PRK13539
cytochrome c biogenesis protein CcmA; Provisional
 31-57 7.26e-03

cytochrome c biogenesis protein CcmA; Provisional


Pssm-ID: 237421 [Multi-domain]  Cd Length: 207  Bit Score: 37.55  E-value: 7.26e-03
                          10        20
                  ....*....|....*....|....*..
gi 1532491334  31 VIIGDNGSGKSTLLRaiTLALLGPVEA 57
Cdd:PRK13539   32 VLTGPNGSGKTTLLR--LIAGLLPPAA 56
ABC_Carb_Monos_I cd03216
First domain of the ATP-binding cassette component of monosaccharide transport system; This ...
 30-48 7.33e-03

First domain of the ATP-binding cassette component of monosaccharide transport system; This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.


Pssm-ID: 213183 [Multi-domain]  Cd Length: 163  Bit Score: 37.02  E-value: 7.33e-03
                          10
                  ....*....|....*....
gi 1532491334  30 HVIIGDNGSGKSTLLRAIT 48
Cdd:cd03216    29 HALLGENGAGKSTLMKILS 47
RloC COG4694
Wobble nucleotide-excising tRNase [Translation, ribosomal structure and biogenesis];
7-66 7.84e-03

Wobble nucleotide-excising tRNase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 443729 [Multi-domain]  Cd Length: 692  Bit Score: 38.56  E-value: 7.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1532491334   7 RISNMKSIDTLDWAIPKDQAAGWHVIIGDNGSGKSTL---LRAITLALLGPVEAAGLRQDWDT 66
Cdd:COG4694     4 KIKKLKNVGAFKDFGWLAFFKKLNLIYGENGSGKSTLsriLRSLELGDTSSEVIAEFEIEAGG 66
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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